Comparison between the ages for the types (after controlling for gender)¶
Questions
- What are the differences between the ages for the different types
- Do we observe the same changes as globally?
Age effect - General Questions
- What are the differences between the ages?
- Which genes and pathways are differentially expressed between 8w and 52w, between 52w and 104w, between 8w and 104w? Are they the same? Is there a gradient?
- Are they different for the two genders?
- Are they different for the two types?
Warning message in is.na(x[[i]]): “is.na() applied to non-(list or vector) of type 'environment'”
========================================================================== * * Package WGCNA 1.63 loaded. * * Important note: It appears that your system supports multi-threading, * but it is not enabled within WGCNA in R. * To allow multi-threading within WGCNA with all available cores, use * * allowWGCNAThreads() * * within R. Use disableWGCNAThreads() to disable threading if necessary. * Alternatively, set the following environment variable on your system: * * ALLOW_WGCNA_THREADS=<number_of_processors> * * for example * * ALLOW_WGCNA_THREADS=4 * * To set the environment variable in linux bash shell, type * * export ALLOW_WGCNA_THREADS=4 * * before running R. Other operating systems or shells will * have a similar command to achieve the same aim. * ========================================================================== Allowing multi-threading with up to 4 threads. [1] "preparing gene to GO mapping data..." [1] "preparing IC data..." [1] "preparing gene to GO mapping data..." [1] "preparing IC data..." [1] "preparing gene to GO mapping data..." [1] "preparing IC data..."
Data¶
Stats¶
| Wald padj < 0.05 | LFC > 0 (Wald padj < 0.05) | LFC < 0 (Wald padj < 0.05) | |
|---|---|---|---|
| 52w VS 8w (SPF) | 1391 | 796 | 595 |
| 52w VS 8w (GF) | 600 | 367 | 233 |
| 104w VS 52w (SPF) | 1474 | 885 | 589 |
| 104w VS 52w (GF) | 1623 | 846 | 777 |
| 104w VS 8w (SPF) | 3231 | 1774 | 1457 |
| 104w VS 8w (GF) | 1861 | 972 | 889 |
Differentially expressed genes¶
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in stack.default(getgo(rownames(l$deg), "mm10", "geneSymbol")): “non-vector elements will be ignored”Warning message in stack.default(getgo(rownames(l$deg), "mm10", "geneSymbol", fetch.cats = "KEGG")): “non-vector elements will be ignored”
Counts¶
52w != 8w or 104w != 8w or 104w != 52w for SPF with abs(FC) > 2
52w != 8w or 104w != 8w or 104w != 52w for GF with abs(FC) > 2
Comparison of the numbers per types¶
Differentially expressed genes
Differentially more expressed genes
Differentially less expressed genes
DEG into gene co-expression network¶
- White: up-regulated
- Black: down-regulated
| 52w VS 8w | 104w VS 52w | 104w VS 8w | |
|---|---|---|---|
| SPF | |||
| GF |
GO analysis¶
Biological process¶
Dot-plot with the most over-represented BP GO (20 most significant p-values for the different comparison)
Network based on description similarity
| 52w VS 8w | 104w VS 52w | 104w VS 8w | |
|---|---|---|---|
| SPF | |||
| GF |
52w VS 8w (SPF)
<!DOCTYPE html>
52w VS 8w (GF)
<!DOCTYPE html>
104w VS 52w (SPF)
<!DOCTYPE html>
104w VS 52w (GF)
<!DOCTYPE html>
Cellular components¶
Dot-plot with the most over-represented CC GO (20 most significant p-values for the different comparison)
Molecular functions¶
Dot-plot with the most over-represented MF GO (20 most significant p-values for the different comparison)
KEGG pathways¶
[1] "Note: 58 of 5406 unique input IDs unmapped." [1] "Note: 58 of 5406 unique input IDs unmapped." [1] "Note: 58 of 5406 unique input IDs unmapped." [1] "Note: 58 of 5406 unique input IDs unmapped." [1] "Note: 58 of 5406 unique input IDs unmapped." [1] "Note: 58 of 5406 unique input IDs unmapped." [1] "Note: 58 of 5406 unique input IDs unmapped." [1] "Note: 58 of 5406 unique input IDs unmapped." [1] "Note: 58 of 5406 unique input IDs unmapped." [1] "Note: 58 of 5406 unique input IDs unmapped." [1] "Note: 58 of 5406 unique input IDs unmapped." [1] "Note: 58 of 5406 unique input IDs unmapped."
[1] "Note: 58 of 5406 unique input IDs unmapped." [1] "Note: 58 of 5406 unique input IDs unmapped."
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Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. 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Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. 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[1] "Note: 58 of 5406 unique input IDs unmapped."
SPF effect in aging¶
Question: Is there any genes that shows an increasing fold change in SPF with aging while not for GF?
| 52w vs 8w for SPF | 52w vs 8w for GF | 104w vs 52w for SPF | 104w vs 52w for GF | Gene number | |
|---|---|---|---|---|---|
| Set 1 | != | != | 244 | ||
| Set 2 | != | == | != | == | 92 |
| 52w VS 8w (SPF) | 52w VS 8w (GF) | 104w VS 52w (SPF) | 104w VS 52w (GF) | 104w VS 8w (SPF) | 104w VS 8w (GF) | |
|---|---|---|---|---|---|---|
| Erg28 | NA | NA | NA | 0.4582787 | NA | 0.3508672 |
| 0610009B22Rik | NA | NA | NA | 0.3173098 | NA | 0.3199247 |
| 0610009L18Rik | NA | NA | NA | NA | -0.7734166 | NA |
| 0610009O20Rik | NA | NA | -0.7088350 | -0.4522004 | -0.4394075 | NA |
| 0610010F05Rik | NA | NA | 0.5226107 | NA | NA | NA |
| 0610010K14Rik | NA | NA | NA | NA | -0.3647340 | NA |
| Gene number | |
|---|---|
| Set 1 | 244 |
| Set 2 | 92 |
Genes with differential expression with aging in SPF but not in GF (set2)¶
52w VS 8w (SPF) > 0 and 104w VS 52w (SPF) > 0¶
[1] 33
Pearson's product-moment correlation
data: mat[, 1] and mat[, 2]
t = 23.489, df = 31, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
0.9456141 0.9867280
sample estimates:
cor
0.9730381
52w VS 8w (SPF) > 0 and 104w VS 52w (SPF) < 0¶
[1] 23
Pearson's product-moment correlation
data: mat[, 1] and mat[, 2]
t = -19.401, df = 21, p-value = 6.881e-15
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
-0.9887658 -0.9368473
sample estimates:
cor
-0.9732205
52w VS 8w (SPF) < 0 and 104w VS 52w (SPF) > 0¶
[1] 24
Pearson's product-moment correlation
data: mat[, 1] and mat[, 2]
t = -8.1923, df = 22, p-value = 3.971e-08
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
-0.9415922 -0.7145938
sample estimates:
cor
-0.8678267
52w VS 8w (SPF) < 0 and 104w VS 52w (SPF) < 0¶
[1] 12
Pearson's product-moment correlation
data: mat[, 1] and mat[, 2]
t = 4.3999, df = 10, p-value = 0.001335
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
0.4459551 0.9453668
sample estimates:
cor
0.8120303
Summary¶
4
5
4
1
